Franklin, in a similar vein to Collingwood counterpart Travis Cloke last year, has postponed talks with the club until the end of the year as he sorts out his football future.
Clarkson told SEN radio on Tuesday morning that clubs and fans would have to get used to high profile players exploring the free agency market.
"It's a delicate situation," Clarkson said.
"Whether it's Hawthorn, other clubs or the football community, I think we've just got to have to get our heads around free agency and how it's going to impact on clubs."
But Clarkson is confident the star forward will remain in the brown and gold in 2014 and beyond.
"He's got a contract at our football club for season 2013 and we're going to do everything we can to ensure that that's good for both of us and we'll see what happens at the end of the year," he said.
"But we're hopeful he'll obviously stay and continue to contribute for the Hawks."
Asked whether he understood Franklin's line of thinking, Clarkson said the forward had every right to assess his future.
"Staying in one place for nine years is a long period of time now, and that's another thing we've just got to get used to," Clarkson said.
"At some point in time he'll sit down with all the information that's available to him, and I think he just genuinely wants to see how this footy season unfolds before he makes a decision on where he wants to play his footy in 2014.
"[There's] a very, very high chance that that's at the Hawthorn footy club."
The Hawks coach also admitted he had his heart in his mouth for his players' welfare during the NAB Cup.
"It's a treacherous time of year and it's a big risk for all players over the next six to eight weeks to get conditioned for four full quarters of AFL footy," he said.
"There's not a hell of a lot you can do about it, but you just have to pray and hope for the best that it's not one of your players who have had a good pre-season."
Clarkson said he and other AFL coaches were concerned at the AFL's trial rule on interchange rotations, saying it was "testing" for clubs and players trying to sort out appropriate game time.
Under a rule that comes into effect from the second round of the NAB Cup, clubs will be permitted to make just 80 rotations for the game, or 20 per quarter.
"The whole priority for preparation for round one is game time and the welfare of the players, not wins or losses, and I think that goes for all 18 clubs," Clarkson said
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Meanwhile, the Hawks coach nominated young midfielder Jed Anderson and Melbourne youngster Jack Viney as his standout AFL Fantasy picks.
Jed Anderson and Jack Viney) are midfielders in AFL Fantasy. Register your team at our AFL Fantasy hub.
Follow AFL Media reporter Ben Guthrie on Twitter at @AFL_BenGuthrie
